MolNFT v1 · #125963 · protein

Structure of coproheme bound hemq from listeria monocytogenes

5LOQ · Putative heme-dependent peroxidase LMO2113: “Structure of coproheme bound hemq from listeria monocytogenes”. X-ray diffraction, 2 ligands (FEC, NA), 20 pockets (best druggability 0.77). MolNFT v1 #125963 on GenesisL1: 3D structure…

PDB: 5LOQ
Type: protein
Length: 1,203 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative heme-dependent peroxidase LMO2113
EC: 1.11.1.-
UniProt: Q8Y5F1
Ligands: FEC, NA
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-)	protein	248	39% helix, 31% strand	Q8Y5F1
B	Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-)	protein	233	42% helix, 32% strand	Q8Y5F1
C	Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-)	protein	237	41% helix, 32% strand	Q8Y5F1
D	Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-)	protein	250	40% helix, 31% strand	Q8Y5F1
E	Putative heme-dependent peroxidase LMO2113 (EC 1.11.1.-)	protein	235	41% helix, 33% strand	Q8Y5F1

Ligands and binding sites

FEC · 1,3,5,8-tetramethyl-porphine-2,4,6,7-tetrapropionic acid ferrous complex · ligand · 5 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 5 copies · chains A, B, E, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, C, B, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	526	0.77	0.84	48	FEC
2	537	0.76	0.83	58	FEC
3	576	0.75	0.82	54	FEC
4	412	0.75	0.84	41	FEC
5	522	0.72	0.81	47	FEC

Interfaces

5 interfaces between chains.

D–E · 1823 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 1822 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 1799 Å² buried · 34 hydrogen bonds · protein-protein
B–E · 1722 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1672 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

5LOQ · Structure of coproheme bound HemQ from Listeria monocytogenes · the same entry in another collection · chain E against E, TM-score 1.00
Q8Y5F1 · AlphaFold monomer V2.0 prediction for coproheme decarboxylase (Q8Y5F1) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8Y5F1
Elsewhere: RCSB PDB 5LOQ · PDBe 5LOQ · UniProt Q8Y5F1

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